I have not experienced this myself.
However, according to other posts in this forum, the chest that follows each EC boss is only available for a limited amount of time after that boss is killed.
Therefore you should never wait another session to clear to the chest after you kill an EC boss. My guess is that it is intended by design, probably to avoid any sort of reset instance /chest farming exploit.. sorry about that.
I guess that makes sense.
oh well, lesson learned.